NOTE: These are the main Street Fighter X Mega Man cheats that are usually applied by pressing down the right key combination. Please find the instructions on how to use these cheats below.

All Eight Bosses, 4 E-Tanks
At the title screen, select Password, then enter this:

All Eight Bosses, 4 E-Tanks: A5, B2, B4, C1, C3, C5, D4, D5, E2

Start new game with 4 E-Tanks (Version with Password only)
Go into password menu, then enter this code. You will start a new game with 4 E-tanks.

Start with 4 E-tanks: A5, B1, B3, C4, D2, D3, E1, E4, E5

Hints

NOTE: As their name suggests hints are not exactly Street Fighter X Mega Man cheats, and are usually just simple (but very useful) tips on how you can unlock secret level, features, find hidden areas and such. Hopefully these will make playing Street Fighter X Mega Man even more entertaining.

Guile's Theme
Pause the game in any level, then hold Jump (default L) and press U D D D (default keys W S S S) to have Guile's Theme replace the background music until you put the code in again.

Hidden Abilities Code
Have the ability to use Hadoken manually without any meter or defeating Ryu.: Press and hold the jump and fire buttons for about 5-6 seconds.

Play as Mega Man without his Helmet
To play as Mega Man without his Helmet, hold shoot on Ryu on the stage select screen and then press Right Right Right Left. If entered correctly, a sound will play and Mega Man will lose his helmet on the stage select screen.

How to get an easy perfect
Just before killing your stage boss, use your E-tank to refill your health back to maximum. Doing this will trick the game into thinking you've earned a perfect in the round. Once you kill your boss when your health is full, you will earn a Perfect.

More E Tanks
If you need more E tanks to beat the game. Just let the timer after you die hit 0, go back into the game and you will have all the tanks you previously collected and you can recollect the E tanks from the levels all over again. I got 10 E tanks at one point.

Fight against Akuma
Complete the game with 3 or more Perfects. After the final battle, Akuma will challenge you.

More E Tanks on Ver. 2.0
Collect the four energy tanks in Chun Li, C. Viper, Ryu, and Dhalsim's stages. After collecting those four, go back to Chun Li's stage and defeat her. After getting the password, write it down and restart the game. When you go back to your game after using the password, go to C. Viper's, Ryu's, and Dhalsim's stages again to get another three energy tanks. You can keep doing this as long as the stage can be played again after entering the password.

Fight Against Sagat
To fight Sagat, you must obtain 4 perfects in the boss rush before Bison. Sagat will show up before the fight with Bison.